1. Field of the Invention
The present invention relates to computer-implemented methods and systems for analyzing the interaction between polypeptide amino acid residues and one or more molecular fragments. The invention further provides methods and systems for using the information regarding the fragment-polypeptide interaction to aid in drug design.
2. Related Art
The action of a particular drug is believed to result from the interaction of that drug with a particular molecular target, such as a protein, nucleic acid, or other molecule found in the biological system. Typical protein drug targets include enzymes and receptors (Thomas G., “Medicinal Chemistry—An Introduction” (John Wiley & Sons, Ltd., New York, 2001)).
In the case of an enzyme, its binding with a drug molecule usually has the effect of interfering with the normal operation of that enzyme. The drug molecule may bind directly within the active site of the enzyme or act indirectly by binding to a so-called allosteric site. Similarly, drugs may act on a receptor by binding to, or near, its surface. This may either activate the receptor, or prevent the binding of its normal substrate to that receptor. Ultimately, such drug actions can result in a physiological response with the purpose of providing a therapeutic effect.
The drug's effectiveness will depend on the stability of the drug-enzyme or drug-receptor complex, as well as the number of binding sites occupied by the drug. Other targets for drug action include nucleic acids and other naturally occurring molecules.
To rationally develop a drug lead, it is therefore desirable to have accurate knowledge of the binding site(s) on the target molecule (e.g., enzyme, receptor or nucleic acid). One method used for determining protein binding sites is so-called protein mapping, where different molecular probes, typically small organic molecules representing various functional groups, are placed around the protein surface to determine the most favorable binding positions (Dennis et al., PNAS 99:4290-4295 (2002)). Experimental approaches to protein mapping include x-ray crystallography and NMR methods. Both of these approaches have shown that probes, even those generally unrelated to any natural substrate of the protein, bind only to a limited number of positions. Generally, a pocket of the active site tends to form a consensus site that binds many ligands, regardless of their sizes and polarities.
Because of major difficulties associated in many cases with co-crystallizing proteins and probes, or using NMR for determining binding sites, a number of methods have been developed to perform mapping computationally rather than experimentally. Examples of such computer codes are the drug design program GRID (Goodford, P. J., J. Med. Chem. 28:849-875 (1985)), or the Multiple Copy Simultaneous Search (MCSS) strategy (Miranker, A. & Karplus, M., Proteins Struct. Funct. Genet. 11:29-34 (1991); Caflish, A., et al., J. Med. Chem. 36:2142-2167 (1993); Joseph-McCarthy, D., et al., J. Am. Chem. Soc. 123:12758-12769 (2001)).
The main problem with the computational approaches referenced above is that they are usually limited to identifying the many local minima along the protein surface of the potential energy field representing the fragment-protein interaction. This data lacks the essential information required for determining which of these minima represents a biologically relevant binding site. (Dennis et al., PNAS 99:4290-4295 (2002)). Indeed, although computationally more expeditious, energy minimization approaches are unable to correctly estimate free energies of binding, which, as presented further on, is the basic biologically relevant quantity for characterizing the binding affinity of a ligand. To estimate a free energy of binding, information on the actual thermodynamic fragment distributions around the protein, i.e., distributions consistent with thermal fluctuations at physiological temperatures, is required. Such thermodynamic distributions provide information on entropic effects, necessary for free energy calculations.
Accordingly, improved computational methods are necessary to provide accurate and efficient estimates of the free energy of binding of molecular fragments to protein binding sites, so that high affinity ligands can be designed for these sites.